Pasha was promoted to Major General on 5 January 2003,[8] and posted as GOC 8th Infantry Division in Sialkot. In April 2005, he was appointed the Commandant of the Command and Staff College in Quetta.[9] From April 2006 to October 2008, Pasha served as the Director General of Military Operations at the Army headquarters overseeing all military engagements in Waziristan, Swat and other tribal areas.[10]

In October 2007, he was selected as the Military Adviser to the Secretary-General of United Nations. However, due to his commitments as DGMO he did not join the United Nations.[11]

In the wake of the 2008 Mumbai attacks, the Indian media reported that President Asif Ali Zardari had instructed Pasha to go to India to share intelligence after a request from Indian Prime Minister Manmohan Singh,[20] which would have constituted the first time a head of the ISI traveling to help the investigation of a terrorist attack.[6] Under pressure from the Pakistan military, the decision was however reversed within a few hours.[21]

In September 2009, he made another public outreach towards India by attending an Iftar party hosted by the then Indian High Commissioner to Pakistan.[22]

Lt. General Pasha was involved in the Memogate controversy of 2011–2012, in which an American businessman, Mansoor Ijaz alleged that a senior Pakistani diplomat, former Amb. Husain Haqqani, had asked him to deliver an unsigned memorandum to Adm. Mike Mullen, chairman of the US Joint Chiefs of Staff at the time. The memorandum sought help from the Obama administration in the wake of the Abbottabad raid during which U.S. Special Forces killed Osama bin Laden. It asked the United States to help avert a military takeover of the civilian government in Pakistan, as well as assistance in executing a Washington insider takeover of the government and military apparatus of Pakistan.

On 10 October 2011, the London Financial Times published an article[23] in which the existence of the memorandum was disclosed,[24] arguing that Pakistan's intelligence services were responsible for fueling Jihadist insurgency in the country. On 22 October 2011, Pasha met Ijaz at the London Intercontinental hotel. The meeting lasted 4 hours, and started a chain of events that ended in a Supreme Court investigation of the Memorandum's origins, authenticity and purpose.[25]

During the London meeting, Pasha was presented with evidence in the form of BlackBerry handset exchanges, written notes and call logs that pointed to the involvement of the senior Pakistani diplomat in the matter.[26] Haqqani continues to deny any involvement with the Memorandum till date.

On 5 April 2012, Pasha agreed to appear before the Judicial Commission constituted by the Supreme Court of Pakistan to examine the available evidence in the memorandum affair. He testified that during the meeting in London, he was shown the same evidence as had appeared during the course of the previous three months of hearings and that he believed the evidence to be factual and authentic. He did not waver in his stance about the purpose, origin or authenticity of the memorandum.

In June 2012, the Judicial Commission released its final conclusions and found that the alleged memorandum was authentic and that former ambassador Husain Haqqani was its "originator and architect". The report said he had in fact sought American support through the memo and wanted to head a new national security team in Pakistan. The report also stated that Haqqani was not loyal to Pakistan as he had left the country, had no material assets in Pakistan and was now living abroad. The Supreme Court, upon hearing the report in session, ordered the former ambassador to appear before the bench. The process of repatriating Haqqani to Pakistan for his appearance in front of the high court continues to the present day.[27]